Simulation and experimental validation of temperature inside PCR reaction chambers of a fully-integrated analytical system

Abstract

This thesis explores the thermal dynamics and heat transfer mechanisms in a fully-integrated thermal PCR system using computational fluid dynamics (CFD) simulations. It examines heat transfer rates and temperature distribution in the reaction chamber, both fully and partially filled with 15µl. Secondary goals include validating simulation models and optimizing experimental setups for accurate temperature monitoring. Utilizing Sulforhodamine B thermo-responsive fluorophore, the study achieves precise temperature measurement during cooling and heating, ensuring three-hour thermal stability. Calibration against Peltier sensors yields an RMSE of 2.04ºC, with mean heating and cooling rate errors of 0.19ºC/s and 0.28ºC/s, respectively. While the results show some discrepancies compared to Sanford's 2014 study , validated against gold-standard thermocouples, they maintain acceptable accuracy. Experimental data align closely with simulations, particularly for cooling rates, confirming the model's accuracy for temperature measurements and ramp rates in a filled reaction chamber. Discrepancies in heating rates highlight some limitations, but overall consistency supports the simulation's validity. The temperature profile was consistent over the cycles. The mean denaturation and elongation temperatures were 93.201 ± 1.366 ºC and 60.896 ± 2.058 ºC in the last cycle of the PCR simulated. And the heating and cooling rates were [CONFIDENTIAL] ± 0.128 ºC/s and [CONFIDENTIAL] ± 0.193 ºC/s. Further analysis reveals that fluid dynamics play a crucial role in determining the temperature distribution and heat transfer efficiency within the simulated reaction chambers. Investigating these dynamics provides insights into optimizing thermal performance and enhancing system reliability. This study establishes simulations as a framework for exploring system modifications and predicting thermal dynamics in the PCR process of the system. Ultimately, this thesis contributes to advancing our understanding of the system and lays groundwork for future innovations in PCR technology.